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        "author": "Aziz Khan",
        "author_email": "azez.khan@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": ".. image:: https://raw.githubusercontent.com/asntech/intervene/master/docs/img/intervene_logo.png\n   \t:target: http://intervene.readthedocs.org\n   \t\nIntervene\n-----------\n\n\ta tool for intersection and visualization of multiple gene or genomic region sets\n\n.. image:: https://travis-ci.org/asntech/intervene.svg?branch=master\n    :target: https://travis-ci.org/asntech/intervene\n\n.. image:: https://img.shields.io/pypi/pyversions/intervene.svg\n    :target: https://www.python.org\n\n.. image:: https://img.shields.io/pypi/v/intervene.svg\n    :target: https://pypi.python.org/pypi/intervene\n\n.. image:: https://anaconda.org/bioconda/intervene/badges/version.svg\n\t:target: https://anaconda.org/bioconda/intervene\n\n.. image:: https://anaconda.org/bioconda/intervene/badges/downloads.svg\n    :target: https://bioconda.github.io/recipes/intervene/README.html\n\n.. image:: https://anaconda.org/bioconda/intervene/badges/installer/conda.svg\n\t:target: https://conda.anaconda.org/bioconda\n\n.. image:: https://img.shields.io/github/issues/asntech/intervene.svg\n\t:target: https://github.com/asntech/intervene/issues\n\n.. image:: https://img.shields.io/twitter/url/https/github.com/asntech/intervene.svg?style=social\n\t:target: https://twitter.com/intent/tweet?text=Intervene%20-%20a%20tool%20for%20intersection%20and%20visualization%20of%20multiple%20genomic%20region%20and%20gene%20sets%20https://github.com/asntech/intervene&url=%5Bobject%20Object%5D\n\nDocumentation\n=============\n\n**A detailed documentation is available in different formats:**  `HTML <http://intervene.readthedocs.org>`_ | `PDF <http://readthedocs.org/projects/intervene/downloads/pdf/latest/>`_ | `ePUB <http://readthedocs.org/projects/intervene/downloads/epub/latest/>`_\n\n.. figure:: http://intervene.readthedocs.io/en/latest/_images/Intervene_sketch.png\n   :width: 800px\n   :align: left\n\nInstallation\n============\n\nQuick installation using Conda\n------------------------------\n\n.. code-block:: bash\n\n\tconda install -c bioconda intervene\n\nThis will install all the dependencies and you are ready to use Intervene.\n\nInstall using `pip`\n-------------------\nYou can install Intervene from PyPi using pip.\n\nInstall from PyPi::\n\n\tpip install intervene\n\nNote: If you install using pip, make sure to install BEDTools and R packages listed below. \n\nIntervene requires the following Python modules and R packages:\n\n\t* Python (=> 2.7 ): https://www.python.org/\n\t* BedTools (Latest version): https://github.com/arq5x/bedtools2\n\t* pybedtools (>= 0.7.9): https://daler.github.io/pybedtools/\n\t* Pandas (>= 0.16.0): http://pandas.pydata.org/\n\t* Seaborn (>= 0.7.1): http://seaborn.pydata.org/\n\t* R (>= 3.0): https://www.r-project.org/\n\t* R packages including UpSetR, corrplot\n\nInstall BEDTools\n----------------\nWe are using pybedtools, which is Python wrapper for BEDTools. So, BEDTools should be installed before using Intervene. It's recomended to have a latest version, but if you have an older version already install, it should be fine.\n\nA quick installation, if you have conda installed.\n\n.. code-block:: bash\n\n    conda install -c bioconda bedtools\n\nPlease read the instructions at https://github.com/arq5x/bedtools2 to install BEDTools, and make sure it is on your path and you are able to call bedtools from any directory.\n\n\nInstall required R packages\n---------------------------\n\nIntervene rquires three R packages, `UpSetR <https://cran.r-project.org/package=UpSetR>`_ , `corrplot <https://cran.r-project.org/package=corrplot>`_ for visualization and `Cairo <https://cran.r-project.org/package=Cairo>`_ to generate high-quality vector and bitmap figures.\n\n.. code-block:: R\n\n    install.packages(c(\"UpSetR\", \"corrplot\", \"Cairo\"))\n\nInstall Intervene from source\n=============================\nYou can install a development version by using ``git`` from GitHub or Bitbucket.\n\n\nInstall development version from `Bitbucket`\n--------------------------------------------\n\nIf you have `git` installed, use this:\n\n.. code-block:: bash\n\n    git clone https://bitbucket.org/CBGR/intervene.git\n    cd intervene\n    python setup.py sdist install\n\nInstall development version from `GitHub`\n-----------------------------------------\nIf you have `git` installed, use this:\n\n.. code-block:: bash\n\n    git clone https://github.com/asntech/intervene.git\n    cd intervene\n    python setup.py sdist install\n\nHow to use Intervene\n====================\nOnce you have installed Intervene, you can type:\n\n.. code-block:: bash\n\n\tintervene --help\n\nThis will show the following help message.\n\n.. code-block:: bash\n\n\tusage: intervene <subcommand> [options]\n\t    \n\tpositional arguments <subcommand>:\n\t  {venn,upset,pairwise}\n\t                        List of subcommands\n\t    venn                Venn diagram of intersection of genomic regions or list sets (upto 6-way).\n\t    upset               UpSet diagram of intersection of genomic regions or list sets.\n\t    pairwise            Pairwise intersection and heatmap of N genomic region sets in <BED/GTF/GFF> format.\n\n\toptional arguments:\n\t  -h, --help            show this help message and exit\n\t  -v, --version         show program's version number and exit\n\n\nto see the help for the three subcommands ``pairwise``, ``venn`` and ``upset`` type:\n\n.. code-block:: bash\n\t\n\tintervene pairwise --help\n\n\tintervene venn --help\n\n\tintervene upset --help\n\nRun Intervene on test data\n--------------------------\n\nTo run Intervene using example data, use the following commands. To access the test data make sure you have ``sudo`` or ``root`` access.\n\n.. code-block:: bash\n\n\tintervene pairwise --test\n\n\tintervene venn --test\n\n\tintervene upset --test\n\nIf you have installed Intervene locally from the source code, you may have problem to find test data. You can download the test data here https://github.com/asntech/intervene/tree/master/intervene/example_data and point to it using ``-i`` instead of ``--test``.\n\n.. code-block:: bash\n\n\t./intervene/intervene venn -i intervene/example_data/ENCODE_hESC/*.bed       \n  \t./intervene/intervene upset -i intervene/example_data/ENCODE_hESC/*.bed      \n  \t./intervene/intervene pairwise -i intervene/example_data/dbSUPER_mm9/*.bed  \n\nThe above three test commands will generate the following three figures (a, b and c).\n\n.. figure:: http://intervene.readthedocs.io/en/latest/_images/Intervene_plots.png\n   :width: 800px\n   :align: left\n\nBy default your results will stored in the current working directory with a folder named ``Intervene_results``. If you wish to save the results in a specific folder, you can type::\n\n\tintervene upset --test --output ~/path/to/your/folder\n\nInteractive Shiny App\n=====================\nIntervene Shiny App is freely available at https://asntech.shinyapps.io/intervene or https://intervene.shinyapps.io/intervene\n\nThe source code for the Shiny app is available at https://github.com/asntech/intervene-shiny\n\nSupport\n========\nIf you have questions, or found any bug in the program, please write to us at ``aziz.khan[at]ncmm.uio.no``\n\nCite Us\n=========\nIf you use Intervene please cite us: ``Khan A, Mathelier A. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets. BMC Bioinformatics. 2017;18:287. doi: 10.1186/s12859-017-1708-7``\n\n",
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